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The 11px difference is the top margin on the h1 that collapses onto the parent container and pulls it downwards. You nust control all the margins and apdding on all the elements you use as this caries between browers.

Code:

h1 {
font-size: medium;
padding: 30px 20px 0px 20px;
margin:0
}

Also what wyrd33 said above makes sense as it is better to float all columns in a fixed width layout and avoid the 3px jog which is making your columns drop right down in ie6 (see faq on floats for more info).